During the postwar occupation of Japan, Harry C. Kelly worked in the Scientific and Technical Division of the Allies' Economic and Scientific Section. During that time, Kelly met and worked with Yoshio Nishina, who was Japan's leading nuclear physicist. Despite discord that existed between the bureaucratic systems of the Allies and the Japanese government, Kelly and Nishina formed a strong relationship of trust, and brought Japan's principal energy agency, RIKEN, back from the abyss of wartime destruction into a new existence as KAKEN. Kelly's youngest staff member, Bowen C. Dees, wrote that their relationship of trust grew gradually into a close friendship that included their families. In 1949 Kelly returned to the United States, and one year later he was appointed as the vice-president of the new US National Science Foundation. For the next ten years he was the chairman of the US delegation to the United States-Japan Committee on Scientific Cooperation, and worked for collaboration in science between the two countries. He continued to make great contributions to the revival of Japanese science. KAKEN was founded on March 1, 1948, and Nishina was its first president. In his speech at the foundation ceremony, Nishina praised Kelly and expressed deep gratitude for his work. "After twenty months, KAKEN has been founded. This is particularly thanks to the efforts and endeavors of Dr. Kelly. His name should long be remembered in the history of this institute." Nishina died in 1951 at the age of 61, and Kelly in 1976, aged 67. That summer, a part of Kelly's ashes was transported from North Carolina and buried in Nishina's grave in Tokyo's Tama cemetery. An inscription was written on the gravestone by Seiji Kaya, the president of the University of Tokyo, formerly of the Honda Laboratory at RIKEN and a friend of both Kelly and Nishina. It says simply, "Harry C. Kelly sleeps here." According to Find-A-Grave contributor Rebecca Ewing Peterson, Kelly married Irene Ermina Jacobs on Dec 14, 1940. Together, they were the parents of Henry Charles Kelly and Thomas Kelly.